Way back when these rules were put in place then the game was basically played between the numbers. So the thinking at the time was probably that when something went all the way out of bounds then it would take a little more time to get the ball set back up for the next play and since the actual game was being "held up" waiting for that then they should stop the clock until the ball got set back into position.
Same reasoning for incomplete passes and first downs. They all result in something a little extra needing to happen before the game could continue. The mechanisms of the game didn't happen nearly as fluidly as they do now so it probably all took a little longer than we're used to seeing for these things to happen.
To further this excellent point, the timing rules are so ingrained into the game that it is not fundamentally proper to go willy-nilly changing them to suit the desires of "saving time." Again, the things that take up the most time in a 4-hour broadcast are the damned commercials.
The Texas H.S. Championships were nice to watch, in that H.S. rules do not cater to TV. Sure, they packed halftime and quarter changes with crass and insipid advertising, and a timeout here and there, but they were for the most part a cleanly played game that lasted under two hours. Could College do this? Sure! The only issue is that TV money rules the game, and they therefore set the rules.
It is important to remember that these TV clowns are not stewards of the game. They could give a parboiled crap about the integrity of the game or anything like that. They only view football as content. Content can be anything, from the
World's Strongest Midget or
The Dog Agility World Championships. It's just a bridge between commercials, and the more viewers they get for that bridging, the more money they can charge for the ads.
With this fact in mind, consider that when you hear some network tool or Sportsradio tool say, "We've got to figure out a way to make games shorter! Why, that Pedo State-Transvestite U. game went four and a half hours last night! It cut into my Midget Olympics broadcast!" What they actually mean is "How can we cut the actual content and shoehorn in more commercials?"